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In the levels, there are certain Pokémon that appear hidden. These Pokémon are signified by a silhouette on the level select page, which shows the Pokémon available, having a blue aura around them. From what I can tell, they unlock through things like getting a high combo, like 30+

Stages 5 & 6 of the zone seem to have special unlock constraints. I just finished Stage 4 of Zone 1 and it unlocked Zone 2 rather than Zone 1's Stage 5. As such, it may be based upon Pokémon capture or score. Will check it out

After beating Zone 3-1, you unlock the Support Pokémon. This allows you to select one Pokémon to place in your party and will make that Pokémon appear in the Trozei board, so you can use its attacks. This allows you to be tactical.

Arceus can be found in the first hidden stage in Zone 8. That Zone is a Sinnoh one for sure. Has Dialga, Palkia and Giratina. Will be making a start on zone listings tonight and will begin screencapping the images